All H.264 .MOV files are in fact standard .MP4 files which has been renamed to .MOV.
The best solution is to simply rename the .MOV files to .MP4 to force it to use another splitter than QuickTime.
From my experience, QuickTime splitter is crap with .MP4 files and I got video/audio desync probably because QuickTime splitter doesn't report the frame rate properly.
I recommend installing gabest's MP4 directshow splitter. After installing this splitter, you will be able to open the renamed .MOV files (now with .MP4 extension) directly in Video Enhancer.
Make sure you have installed DirectShow codec for H.264 such as ffdshow.
In fact, there is a MP4 plugin for VirtualDub and if you install the plugin in VirtualDub, you can edit MP4 files directly in VirtualDub as well. The only drawback is that you can only save the files as .AVI though. But there are ways to convert those .AVI files back to standard .MP4 files but it's a complicated process.
One HUGE problem with editing in VirtualDub is if your MP4 files contain AAC audio. VirtualDub and the AVI file format does not support AAC audio, so you will loose the audio.
I recommend Avidemux for editing non AVI files. It'll open and save in many formats and the editing is similar to VirtualDub.
Download the MP4 splitter here:
http://sourceforge.net/project/showfiles.php?group_id=205650&package_id=246121&release_id=541146In order to install it, just open command prompt in the folder where you have unzipped the MP4Splitter.ax file and type this into the command line:
regsvr32 MP4Splitter.ax
Do not delete the MP4Splitter.ax and it must stay in the folder where you put it.